Y-Cable with Int Encoder?

We want to expand to 12 motors and are thinking about using a Y-cable for the left drive train and another Y-cable for the right drive train. Each side has two motors. I currently have Integrated Encoders on the drive motors. I actually only need one of the integrated encoders in the program so I can get rid of the other three. Can an integrated encoder be used when it is only on one motor while using a Y-cable to power two motors…? How would that work?